This presentation describes the SPIRE project, a distributed, interdisciplinary research project that is exploring how the Semantic Web can be used in Ecoinformatics. Several tools are described including the Swoogle Semantic Web search engine and ELVIS (the Ecosystem Location Visualization and Information System), a suite of tools for constructing food webs for a given location. The presentation shows how the SPIRE tools are used to answer queries against multiple Semantic Web documents in the course of building a food web model.